Suddenly, Jean Grey awakens in a mysterious place, an alternate reality. Ironman appears before her. Thinking that Ironman is dead after seeing him sacrifice himself (in the battle with Onslaught), Jean lashes out with her telekinetic blasts. When Ironman attempts to retaliate, Jean feels she is being pulled back by an invisible force, and she disappears from Ironman’s sight.
Deep in the mountains in Colorado, two hikers spot two planes in the air, one (Operation: Zero Tolerance) attacking another (X-Men). Jean awakens as their plane is crashing. Storm and Jean are using their powers to hold the plane intact for Scott to land. Cannonball fires up and attacks Zero Tolerance’s aircraft. Unknown to the X-Men, Cannonball’s counterattack is being televised and labelled as a terrorist attack.
Henry Gyrich is being interviewed for television regarding the X-Men’s attack. He reveals that Operation: Zero Tolerance is “a task force...determined to contain the mutant menace once and for all”. He tries to convince that the X-Men are a threat, referencing Onslaught’s murder of thirty-four citizens (including Captain America, the Avengers and the Fantastic Four), the Legacy virus previously known only to infect mutants now infects humans as well, the assassination of Graydon Creed and a slew of mutant related “threats”.
Back in Colorado, Cannonball continues to be attacked, this time by Sentinels, making him unable to destroy Zero Tolerance’s aircraft. Cyclops takes a point blank shot at the aircraft but gets blasted out of his pilot’s seat instead and apprehended by the Sentinels. The following X-Men, Storm, Cannonball, Wolverine and Phoenix are subsequently captured as well.
At that time, the New York state police converge on the Xavier Institute to wait for the Feds to arrive. The Feds arrive in the form of Sentinels.
Bobby Drake who is home to be with his injured father, feels compelled to help his comrades. His father has defended Bobby in the past leading to his injury, encourages Bobby to go.
Bastion, head of the “anti-mutant task force” Operation: Zero Tolerance, leads the siege of the Xavier Institute. He is also holding Charles Xavier imprisoned in a facility in New Mexico. Xavier is horrified as he watches the holographic projection of Bastion retrieving confidential information from the Institute’s “War Room”.